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Iso-seq analysis and functional annotation of the Santa Fe cave crayfish (Procambarus erythrops) transcriptome Mar. Genom. (IF 1.672) Pub Date : 2021-01-21 Celine M. Carneiro; Jerald D. Noble; Adele Pietras; Paul Moler; James D. Austin
The genus Procambarus represents a diverse genus of freshwater crayfish that includes epigean species, stygobitic species, and at least one parthenogenic species. Despite its evolutionary, ecological, and economic importance, most genomic and transcriptomic resources for this genus are limited to a couple of model species. We sequenced the transcriptome of a non-model species, P. erythrops, a geographically
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De novo transcriptome assembly, functional annotation and characterization of the Atlantic bluefin tuna (Thunnus thynnus) larval stage Mar. Genom. (IF 1.672) Pub Date : 2020-12-26 Luca Marisaldi; Danilo Basili; Giorgia Gioacchini; Adriana Canapa; Oliana Carnevali
In the present work, we assembled and characterized a de novo larval transcriptome of the Atlantic bluefin tuna Thunnus thynnus by taking advantage of publicly available databases with the goal of better understanding its larval development. The assembled transcriptome comprised 37,117 protein-coding transcripts, of which 13,633 full-length (>80% coverage), with an Ex90N50 of 3061 bp and 76% of complete
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Complete genome sequence of Janibaecter indicus YB324 from an Atlantic marine sediment Mar. Genom. (IF 1.672) Pub Date : 2020-12-17 Shengxiang Pei; Fuquan Xie; Rui Zhang; Gaiyun Zhang
Janibacter indicus YB324, a gram-positive, aerobic and non-motile actinobacterium isolated from south Atlantic sediment at a depth of 2875 m. The complete genome sequence of the strain YB324 was obtained using PacBio Sequel HGAP.4 and comprised of 3,369,845 base pairs with a 71.3 mol% G + C content, 3225 protein-coding genes, 53 RNAs. In silico analysis confirmed the genes associated with polysaccharide
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The complete genome of extracellular protease-producing Deinococcus sp. D7000 isolated from the hadal region of Mariana Trench Challenger Deep Mar. Genom. (IF 1.672) Pub Date : 2020-11-30 Ru-Yi Zhang; Ying Huang; Wen-Jing Qin; Zhe-Xue Quan
The general features and genomic characteristics of gram-positive Deinococcus sp. D7000 isolated from the hadal region of Mariana Trench Challenger Deep were analyzed in this study. Deinococcus sp. D7000 has a genome consisting of 4,558,742 bp, including one chromosome and nine plasmids. This strain exhibits extracellular protease activity under low temperatures. Among 4328 protein-coding sequences
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Regulation of globin expression in Antarctic fish under thermal and hypoxic stress Mar. Genom. (IF 1.672) Pub Date : 2020-11-26 Daniela Giordano; Paola Corti; Daniela Coppola; Giovanna Altomonte; Jianmin Xue; Roberta Russo; Guido di Prisco; Cinzia Verde
In the freezing waters of the Southern Ocean, Antarctic teleost fish, the Notothenioidei, have developed unique adaptations to cope with cold, including, at the extreme, the loss of hemoglobin in icefish. As a consequence, icefish are thought to be the most vulnerable of the Antarctic fish species to ongoing ocean warming. Some icefish also fail to express myoglobin but all appear to retain neuroglobin
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Complete genome sequence of Micromonospora craniellae LHW63014T, a potential metal ion-chelating agent producer Mar. Genom. (IF 1.672) Pub Date : 2020-11-05 Xue Yang; Zhong-Hui Zhu; Xia Ji; Zhao-Ming Liu; Hua Zhang; Bin Wei
Micromonospora craniellae LHW63014T is a novel marine Micromonospora, isolated from a Craniella species sponge collected in the South China Sea. In this study, we report the complete genome sequence of M. craniellae LHW63014T, which is comprised of a circular chromosome of 6,839,926 bp with the G + C content of 70.9 mol%. The complete genome contained 6572 protein-coding genes, 48 tRNA genes, and 9
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Complete genome sequence of Marinomonas arctica BSI20414, a giant antifreeze protein-producing bacterium isolated from Arctic sea ice Mar. Genom. (IF 1.672) Pub Date : 2020-11-02 Li Liao; Shanhui Gao; Yi Xu; Shiyuan Su; Jiao Wen; Yong Yu; Bo Chen
Sea ice in the polar oceans is a dynamic and challenging environment for life to survive, with extreme gradients of temperature, salinity and nutrients etc., as well as formation of ice crystals. Bacteria surviving in sea ice attract broad attention from academia and industry, due to fascinating mechanisms for adaptation. Here we described the complete genome sequence of Marinomonas arctica BSI20414
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Skin distress associated with xenobiotics exposure: An epigenetic study in the Mediterranean fin whale (Balaenoptera physalus) Mar. Genom. (IF 1.672) Pub Date : 2020-10-15 Annalaura Mancia; Luigi Abelli; Maria Cristina Fossi; Cristina Panti
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A first genomic portrait of the Florida stone crab Menippe mercenaria: Genome size, mitochondrial chromosome, and repetitive elements Mar. Genom. (IF 1.672) Pub Date : 2020-10-04 J. Antonio Baeza
The Florida stone crab, Menippe mercenaria, is an ecologically relevant species in shallow water hard-bottom environments and a target of a profitable fishery in the western Atlantic. Using low coverage short Illumina 250 bp pair-end reads sequencing, this study reports, for the first time, the genome size, mitochondrial chromosome, and nuclear repetitive elements, including microsatellites, in M.
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Transcriptome expression profiles between diploid and triploid Pacific abalone (Haliotis discus hannai) juveniles in response to acute heat-stress and hypoxia treatments Mar. Genom. (IF 1.672) Pub Date : 2020-10-01 Chan-Hee Kim; Eun Jeong Kim; Chaehwa Seo; Choul Ji Park; Yoon Kwon Nam
With an increasing interest for the use of triploids in abalone aquaculture, it is crucial to understand their physiological responses to environmental stress, particularly such as heat-stress and hypoxia, which are significant factors that cause adverse effects on the efficiency and capacity of farming practice in abalone production. However, nothing is known about gene expression of triploid abalone
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Genomic analysis of Microbacterium sediminis YLB-01T reveals backgrounds related to its deep-sea environment adaptation Mar. Genom. (IF 1.672) Pub Date : 2020-09-15 Zhiwei Yi; Xiaorong Cao; Hong Li; Huahua Jian; Xiashutong Xu; Libo Yu; Xixiang Tang
Microbacterium sediminis YLB-01T, a piezotolerant and psychrotolerant actinomycete, was isolated from deep-sea sediment of the South-West Indian Ocean and could be a good model for understanding the adaptation of extremophiles to the benthic piezosphere. Here, we report the analysis of the complete genome sequence of strain YLB-01T. The genome sequence consists of a single circular chromosome comprising
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First transcriptome assembly of a newly discovered vent mussel, Gigantidas vrijenhoeki, at Onnuri Vent Field on the northern Central Indian Ridge. Mar. Genom. (IF 1.672) Pub Date : 2020-09-12 Taewoo Ryu,Jong Guk Kim,Jimin Lee,Ok Hwan Yu,Seungshic Yum,Dongsung Kim,Seonock Woo
This is the first report of a transcriptome assembly of a newly discovered hydrothermal vent mussel, Gigantidas vrijenhoeki (Bivalvia: Mytilidae), on the Central Indian Ridge. Gigantidas vrijenhoeki was identified from material collected at the newly discovered Onnuri Vent Field (OVF) on the Central Indian Ridge in 2018, and was reported as a new species, distinct from another dominant hydrothermal
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Seasonal gene expression profiling of Antarctic krill in three different latitudinal regions. Mar. Genom. (IF 1.672) Pub Date : 2020-08-07 Flavia Höring,Alberto Biscontin,Lars Harms,Gabriele Sales,Christian S Reiss,Cristiano De Pittà,Bettina Meyer
The Antarctic krill, Euphausia superba, has evolved seasonal rhythms of physiology and behaviour to survive under the extreme photoperiodic conditions in the Southern Ocean. However, the molecular mechanisms generating these rhythms remain far from understood. The aim of this study was to investigate seasonal differences in gene expression in three different latitudinal regions (South Georgia, South
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Complete genome sequence of a piezophilic bacterium Salinimonas sediminis N102T, isolated from deep-sea sediment of the New Britain Trench Mar. Genom. (IF 1.672) Pub Date : 2020-08-07 Junyi Xue; Jiasong Fang; Hongge Zhang; Yuli Wei; Li Wang; Rulong Liu; Junwei Cao
Salinimonas sediminis N102T is a cold-adapted, slightly halophilic piezophile isolated from deep-sea sediment (4700 m) of the New Britain Trench. In this study, we report the complete genome sequence of S. sediminis N102T, which is comprised of 4,440,293 base pairs with a mean G + C content of 48.2 mol%. The complete genome harbors 3851 predicted protein-coding genes, 70 tRNA genes and 15 rRNA genes
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Complete genome sequence of an Arctic Ocean bacterium Shewanella sp. Arc9-LZ with capacity of synthesizing silver nanoparticles in darkness. Mar. Genom. (IF 1.672) Pub Date : 2020-08-07 Shuang Li,Yuanyuan Niu,Hao Chen,Peiqing He
Shewanella sp. Arc9-LZ is a bacterium capable of synthesizing silver nanoparticles in darkness. It was isolated from the marine sediment from the Arctic Ocean (158°01′12”W; 84°28′38”N) collected during the 9th Chinese National Arctic Expedition in 2018. Here, we describe the complete genome of Shewanella sp. Arc9-LZ. The complete genome of Shewanella sp. Arc9-LZ is composed of a circular chromosome
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Complete genome sequence of a high cesium ion- tolerating bacterium Bacillus sp. Cs-700 isolated from the South China Sea sediment. Mar. Genom. (IF 1.672) Pub Date : 2020-08-05 Fei Zhang,Yaping Guo,Jianda Ji,Guangyu Li,Huangkai Zhang,Tao Yu
Generally, cesium ion (Cs+) which concentration of above the millimolar order is toxic to microorganisms. In this study we report the isolation and genomic characteristics of Bacillus sp. Cs-700, which can grow in media supplemented with 700 mM Cs+ and was one of the most Cs+ tolerating bacteria been reported. Bacillus sp. Cs-700 was isolated from the South China Sea, and comprised one circular chromosome
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The Atlantic salmon whole blood transcriptome and how it relates to major locus maturation genotypes and other tissues Mar. Genom. (IF 1.672) Pub Date : 2020-07-31 Samuel C. Andrew; Craig R. Primmer; Paul V. Debes; Jaakko Erkinaro; Jukka-Pekka Verta
The Atlantic salmon (Salmo salar) is important to many ecosystems and local economies and has therefore become the focus of a broad range of research questions that have benefited from the availability of high-quality genomic resources. Albeit gene expression studies have been extensive for this species, the transcriptome information for Atlantic salmon whole blood has been lacking. A transcriptome
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First de novo transcriptome assembly of Iwagaki oyster, Crassostrea nippona, and comparative evolutionary analysis of salinity-stress response genes in Crassostrea oysters Mar. Genom. (IF 1.672) Pub Date : 2020-07-25 Jianwen Gong; Qi Li; Hong Yu; Shikai Liu; Lingfeng Kong
Crassostrea nippona is a commercially important oyster species in East Asia for it is edible during the summer when the other oyster species are unavailable. Salinity is one of the important limiting factors to the survival and distribution of this stenohaline species. In this study, 535 million reads (74G data) from C. nippona were produced and assembled into 66,742 transcripts. The number of 19,253
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Complete genome sequence of Alteromonas pelagimontana 5.12T, a marine exopolysaccharide-producing bacterium isolated from hydrothermally influenced deep-sea sediment of eastern Southwest Indian Ridge. Mar. Genom. (IF 1.672) Pub Date : 2020-07-19 Rupesh Kumar Sinha,K P Krishnan,P John Kurian
The whole genome of Alteromonas pelagimontana 5.12T, a psychrotolerant deep-sea bacterium isolated from the sediment sample of eastern Southwest Indian Ridge, was sequenced and analysed for understanding its metabolic capacities and biosynthesis potential of natural products. The circular genome contained 4.3 Mb with a GC content of 42.6 mol%. Genomic data mining revealed a gene cluster for heavy metal
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Complete genome sequence of Thermosulfurimonas marina SU872T, an anaerobic thermophilic chemolithoautotrophic bacterium isolated from a shallow marine hydrothermal vent. Mar. Genom. (IF 1.672) Pub Date : 2020-07-11 Maxime Allioux,Mohamed Jebbar,Galina Slobodkina,Alexander Slobodkin,Yann Moalic,Anastasia Frolova,Zongze Shao,Karine Alain
Thermosulfurimonas marina strain SU872T is a thermophilic, anaerobic, chemolithoautotrophic bacterium, isolated from a shallow-sea hydrothermal vent in the Pacific Ocean near Kunashir Island, that is able to grow by disproportionation of inorganic sulfur compounds and dissimilatory nitrate reduction to ammonium. Here we report the complete genome sequence of strain SU872T, which presents one circular
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Complete genome sequence of Streptomyces sp. SCSIO 03032 isolated from Indian Ocean sediment, producing diverse bioactive natural products Mar. Genom. (IF 1.672) Pub Date : 2020-07-09 Liang Ma; Wenjun Zhang; Zhiwen Liu; Yanbing Huang; Qingbo Zhang; Xinpeng Tian; Changsheng Zhang; Yiguang Zhu
Streptomyces sp. SCSIO 03032, isolated from a deep-sea sediment sample (−3412 m) from the Indian Ocean, produces several classes of bioactive compounds including α-pyridone antibiotics (piericidins), polycyclic macrolactams (heronamides) and bisindole alkaloids (spiroindimicins, indimicins and lynamicins). Here we report the complete genome sequence of Streptomyces sp. SCSIO 03032, which consists of
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Complete genome sequence of Exiguobacterium mexicanum A-EM, isolated from seafloor hydrothermal vents in Atlantic Ocean. Mar. Genom. (IF 1.672) Pub Date : 2020-07-01 Jilin Lei,Minggang Zheng,Ling Wang,Guobin Yin,Yinghua Lou,Lei Shi
Exiguobacterium mexicanum A-EM was isolated from seafloor hydrothermal vents(Caifan field, 14.0S 14.4 W) and was shown to degrade toxins and contaminants. Here, we present the complete genome sequence of A-EM, consisting of 2,412,492 bp, with a GC content of 53.16%. A-EM sequence contains genes encoding enzymes that degrade toxins and contaminants. Complete genome sequence of the strain A-EM can further
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Complete genome sequence of a marine-derived bacterium Pseudomonas sp. SXM-1 and characterization of its siderophore through antiSMASH analysis and with mass spectroscopic method Mar. Genom. (IF 1.672) Pub Date : 2020-06-30 Wenbin Guo; Fang Li; Jinmei Xia; Weiyi Wang
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De novo transcriptome assembly for Pachygrapsus marmoratus, an intertidal brachyuran crab. Mar. Genom. (IF 1.672) Pub Date : 2020-06-22 Sara Pinosio,Sara Fratini,Stefano Cannicci,Matteo Oliva,Carlo Pretti,Mariella Baratti
The marble crab Pachygrapsus marmoratus inhabits the rocky shores of the Mediterranean Sea, Black Sea and East Atlantic Ocean. As other intertidal species, it is considered a model species to study the effects of environmental stressors on natural populations. In this study, we performed Illumina next-generation sequencing on eleven P. marmoratus specimens with the aims to (i) reconstruct their whole
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Genomic insights into antioxidant activities of Pyruvatibacter mobilis CGMCC 1.15125T, a pyruvate-requiring bacterium isolated from the marine microalgae culture Mar. Genom. (IF 1.672) Pub Date : 2020-06-19 Jin-Cheng Rong; Bo-Wen Ji; Ning Zheng; Zhong-Zhi Sun; Yi-Song Li; Bin-Bin Xie
Pyruvate is a well-known scavenger of reactive oxygen species (ROS) like hydrogen peroxide and could prevent cells from oxidative damage. A pyruvate-requiring marine bacterium, Pyruvatibacter mobilis CGMCC 1.15125T (=KCTC 42509T), was isolated from the culture broth of a photosynthetic marine microalga. Here we report the complete genome sequence of Pyruvatibacter mobilis, which contained a circular
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Complete genome sequence of Paenibacillus xylanexedens PAMC 22703, a xylan-degrading bacterium. Mar. Genom. (IF 1.672) Pub Date : 2020-06-18 Junsang Hwang,Seung Chul Shin,Jae Won Han,Sang Pil Hong,Won-Ki Min,Donghwa Chung,Hyo Jin Kim
Paenibacillus is widely distributed in various environments and has the potential for use as a biotechnological agent in industrial processes. Here, we report the complete genome sequence of the marine bacterium, Paenibacillus xylanexedens PAMC 22703, which utilizes xylan. The P. xylanexedens PAMC 22703 strain was isolated from marine sediments. P. xylanexedens PAMC 22703 utilizes xylan as a carbon
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New bacterial and archaeal lineages discovered in organic rich sediments of a large tropical Bay. Mar. Genom. (IF 1.672) Pub Date : 2020-06-17 Diogo A Tschoeke,Felipe H Coutinho,Luciana Leomil,Giselle Cavalcanti,Bruno S Silva,Gizele D Garcia,Leandro Candeia Dos Anjos,Larissa Borges Nascimento,Luciane S Moreira,Koko Otsuki,Renato C Cordeiro,Carlos E Rezende,Fabiano L Thompson,Cristiane C Thompson
The nutrient and oxygen gradient present in marine sediments promotes high levels of microbial diversity. We applied metagenomics and biogeochemical tools to analyze microbial communities in different sediment depths (0–4 m below sea floor, mbsf) from Guanabara Bay, Brazil, a brackish tropical ecosystem with a history of massive anthropogenic impacts, and a largely unknown sediment microbial diversity
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Complete genome of Polaromonas vacuolata KCTC 22033T isolated from beneath Antarctic Sea ice. Mar. Genom. (IF 1.672) Pub Date : 2020-06-17 Kyuin Hwang,Hanna Choe,Arshan Nasir,Kyung Mo Kim
Polaromonas vacuolata KCTC 22033T is an obligate aerobic, Gram-negative, psychrophilic and rod-shaped bacterium isolated from beneath the sea ice off the coast of the Palmer Peninsula, Anvers Islands, Antarctica. P. vacuolata is the type species of Polaromonas genus and the first example of gas vacuolate Betaproteobacteria isolated from marine habitats. Here, we report a complete genome of P. vacuolata
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Genomic analysis of Brevundimonas mediterranea D151-2-6 isolated from hadal sediment of the Pacific Ocean. Mar. Genom. (IF 1.672) Pub Date : 2020-06-16 Siyuan Wang,Libo Yu,Xiaoli Tan,Xiaorong Cao,Xixiang Tang,Huahua Jian
Brevundimonas mediterranea D151-2-6 is a marine bacterium that has been isolated from 6582-m hadal sediment of the Pacific Ocean. Here, we present the complete genome sequence of B. mediterranea D151-2-6. The genome of strain D151-2-6 is 3,383,373 base pairs in size. It contains one circular chromosome with an average G + C content of 67.41%, 53 tRNAs, and 3270 protein-coding genes. Genomic analysis
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Genome analysis of Thermosulfuriphilus ammonigenes ST65T, an anaerobic thermophilic chemolithoautotrophic bacterium isolated from a deep-sea hydrothermal vent Mar. Genom. (IF 1.672) Pub Date : 2020-06-04 Galina Slobodkina; Maxime Allioux; Alexander Merkel; Karine Alain; Mohamed Jebbar; Alexander Slobodkin
Thermosulfuriphilus ammonigenes ST65T is an anaerobic thermophilic bacterium isolated from a deep-sea hydrothermal vent chimney. T. ammonigenes is an obligate chemolithoautotroph utilizing elemental sulfur as an electron donor and nitrate as an electron acceptor with sulfate and ammonium formation. It also is able to grow by disproportionation of elemental sulfur, thiosulfate and sulfite. Here, we
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Full-length transcriptome analysis of Misgurnus anguillicaudatus Mar. Genom. (IF 1.672) Pub Date : 2020-05-26 Wei Luo; Qing Wu; Tianzhu Wang; Zhou Xu; Dongjie Wang; Yan Wang; Song Yang; Yuejin Long; Zongjun Du
Faithful analysis of transcripts represents a critical component of the gene discovery, genomic characterization and annotation process in species without a reference genome. The present study generated 28,001 full-length transcripts of Misgurnus anguillicaudatus using the Pacific Bioscience (PacBio) single-molecule real-time (SMRT) sequencing system. A total of 77,346 consensus isoforms were identified
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De novo assembly and annotation of the transcriptome of Astyanax lacustris liver unveil candidate genes to monitor response to environmental stress Mar. Genom. (IF 1.672) Pub Date : 2020-05-25 Karla Giavarini Gnocchi; Johara Boldrini-França; Levy Carvalho Gomes; Adriana Regina Chippari-Gomes
Astyanax lacustris is a freshwater characid fish species that inhabits small streams, lakes and rivers in South America. These fish are abundant in the wild and highly adaptable in captive, being considered a good model for ecotoxicological studies. Nevertheless, there are only shortcoming gene sequence information available in public databases, which hinder their use in more comprehensive investigations
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De novo assembly and functional annotation of the heart + hemolymph transcriptome in the Caribbean spiny lobster Panulirus argus. Mar. Genom. (IF 1.672) Pub Date : 2020-05-12 J Antonio Baeza,Matthew MacManes
The spiny lobster, Panulirus argus, is an ecologically relevant species in shallow water coral reefs and a target of the most lucrative fishery in the greater Caribbean region. This study reports, for the first time, the heart + hemolymph transcriptome of the Caribbean spiny lobster Panulirus argus assembled from short Illumina 150 bp PE raw reads. A total of 80,152,094 raw reads were assembled using
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Whole genome sequencing of four bacterial strains from South Shetland Trench revealing biosynthetic and environmental adaptation gene clusters. Mar. Genom. (IF 1.672) Pub Date : 2020-05-06 Wael M Abdel-Mageed,Burhan Lehri,Scott A Jarmusch,Kevin Miranda,Lamya H Al-Wahaibi,Heather A Stewart,Alan J Jamieson,Marcel Jaspars,Andrey V Karlyshev
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Sex-specific gene expression differences in reproducing Syllis prolifera and Nudisyllis pulligera (Annelida, Syllidae) Mar. Genom. (IF 1.672) Pub Date : 2020-04-11 Guillermo Ponz-Segrelles; Rannyele Passos Ribeiro; Christoph Bleidorn; María Teresa Aguado Molina
Syllidae is an annelid family characterized by its complex life cycles involving some of the most outstanding annelid reproductive strategies. Syllid reproductive modes sometimes imply the modification of the posterior body to form independent reproductive units (schizogamy) or the development of swimming adults (epigamy). These modes of sexual reproduction have been studied for more than 150 years
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Large-scale analysis of zebrafish (Danio rerio) transcriptomes identifies functional modules associated with phenotypes. Mar. Genom. (IF 1.672) Pub Date : 2020-04-07 Wei Liu,Yanan Wang
Zebrafish (Danio rerio) is an excellent model for biomedicine research due to its genetic accessibility and optical transparency. A large number of microarray based transcriptomes of zebrafish have been profiled in various cell types, tissues, development stages, toxicological exposures and other conditions. However, there is still no easy-to-use web tool to explore those precious data. We downloaded
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Complete genome sequence of Bacillus sp. N1-1, a κ-selenocarrageenan degrading bacterium isolated from the cold seep in the South China Sea Mar. Genom. (IF 1.672) Pub Date : 2020-04-06 Kai Wang; Yang Zhao; Xixi Wang; Changfeng Qu; Jinlai Miao
κ-Selenocarrageenan is made from natural κ-carrageenan, in which Se partially replaces Sulfur (S). The underlying mechanism of κ-selenocarrageenan degradation remain unreported so far. Here, we describe the complete genome of a cold seep bacterium, Bacillus sp. N1-1, which can degrade κ-selenocarrageenan. The strain has a circular genome of 4,497,340 bp and 40.48 mol% G + C content, consisting of 4272
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Complete genome of Sulfitobacter sp. BSw21498 isolated from seawater of Arctic Kongsfjorden. Mar. Genom. (IF 1.672) Pub Date : 2020-03-27 Yin-Xin Zeng,Yi-He Zhang,Hui-Rong Li,Wei Luo
The genus Sulfitobacter has been mostly found in marine and hypersaline environments. Members of this genus were observed to be associated with marine microalgae by inducing cell death of algae and degrading of algae-derived dimethylsulfoniopropionate (DMSP). Here we reported the complete genome sequence of strain Sulfitobacter sp. BSw21498 isolated from seawater of Kongsfjorden, an Arctic fjord in
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Complete genome sequence of Methanofervidicoccus sp. A16, a thermophilic methanogen isolated from Mid Cayman Rise hydrothermal vent. Mar. Genom. (IF 1.672) Pub Date : 2020-03-26 Liping Wang,Qiliang Lai,Mohamed Jebbar,Zongze Shao,Karine Alain
Methanofervidicoccus sp. A16 is a novel thermophilic and obligate hydrogenotrophic methanogen isolated from a deep-sea hydrothermal vent chimney sample at the Mid Cayman spreading center, Caribbean Sea. Here we report the complete genome of strain A16, which has one circular chromosome of 1,485,358 bp with a mean G+C content of 35.01 mol%. The complete genome harbors 1442 predicted protein-encoding
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Genomic characterization of filamentous phage vB_VpaI_VP-3218, an inducible prophage of Vibrio parahaemolyticus. Mar. Genom. (IF 1.672) Pub Date : 2020-03-12 Alexa Garin-Fernandez,Frank Oliver Glöckner,Antje Wichels
The seawater temperature rise can promote the growth of potentially pathogenic Vibrio species. In the North Sea, V. parahaemolyticus strains have been isolated and characterized. These strains contain prophages that may contribute to the emergence of pathogenic strains in the marine environment. Here, we present the genome structure and possible biological functions of the inducible phage vB_VpaI_VP-3218
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Complete genome sequence of Anoxybacter fermentans DY22613T, a piezophilic dissimilatory Fe(III)-reducing bacterium isolated from East Pacific Rise hydrothermal sulfides. Mar. Genom. (IF 1.672) Pub Date : 2020-03-07 Xi Li,Donghua Qiu,Xiang Zeng,Zongze Shao
Anoxybacter fermentans DY22613T is a novel piezophilic dissimilatory iron(III)-reducing bacterium isolated from East Pacific Rise (EPR) hydrothermal sulfides. The strain shows very low 16S rRNA gene similarity (86.92%) with the Halanaerobiales, and represents at least a novel genus Anoxybacter within the class Clostridia. Here, we describe the first complete genome of strain DY22613T in this genus
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Complete genome sequence of Neptunomonas concharum JCM17730T: An acetate assimilating bacterium isolated from a dead ark clam. Mar. Genom. (IF 1.672) Pub Date : 2020-02-28 Nan Pu,Wei Li,Zheng-Jun Li
The marine bacterium Neptunomonas concharum was firstly characterized in 2012. It preferred to utilize acetate as the carbon source to accumulate poly-3-hydroxybutyrate (PHB) as intracellular carbon and energy storage. Here we report the genomic characteristics of N. concharum JCM17730T. The complete genome sequence of N. concharum JCM17730T consists of 3,561,992 bp in one contig, without plasmid.
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The genome of the sea anemone Actinia equina (L.): Meiotic toolkit genes and the question of sexual reproduction Mar. Genom. (IF 1.672) Pub Date : 2020-02-11 Craig S. Wilding, Nicola Fletcher, Eleanor K. Smith, Peter Prentis, Gareth D. Weedall, Zac Stewart
The beadlet anemone Actinia equina (L.) (Cnidaria: Anthozoa: Actiniaria: Actiniidae) is one of the most familiar organisms of the North European intertidal zone. Once considered a single, morphologically variable species across northern Europe, it is now recognised as one member of a variable species complex. Previous studies of distribution, aggression, allozymes and mitochondrial DNA suggest that
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Improved genomic resources for the black tiger prawn (Penaeus monodon) Mar. Genom. (IF 1.672) Pub Date : 2020-02-04 Dong Van Quyen, Han Ming Gan, Yin Peng Lee, Dinh Duy Nguyen, Thi Hoa Nguyen, Xuan Thach Tran, Van Sang Nguyen, Dinh Duy Khang, Christopher M. Austin
World production of farmed crustaceans was 7.8 million tons in 2016. While only making up approximately 10% of world aquaculture production, crustaceans are generally high-value species and can earn significant export income for producing countries. Viet Nam is a major seafood producing country earning USD 7.3 billion in 2016 in export income with shrimp as a major commodity. However, there is a general
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The chloroplast genome sequence of the green macroalga Caulerpa okamurae (Ulvophyceae, Chlorophyta): Its structural features, organization and phylogenetic analysis Mar. Genom. (IF 1.672) Pub Date : 2020-02-01 Fengrong Zheng, Bo Wang, Zhen Shen, Zongxing Wang, Wei Wang, Hongzhan Liu, Claire Wang, Maosheng Xin
To clarify evolutionary characteristics, phylogenetic relationships as well as species identification of C. okamurae, we determined the cpDNA sequence of Caulerpa okamurae using de novo sequencing in the present study. The cpDNA of C. okamurae was 148,274 bp in length, and it lacked the inverted repeat commonly found in vascular green plants. The cpDNA of C. okamurae was highly compact with a gene
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A comprehensive non-redundant reference transcriptome for the Atlantic silverside Menidia menidia. Mar. Genom. (IF 1.672) Pub Date : 2020-01-25 Nina Overgaard Therkildsen,Hannes Baumann
The Atlantic silverside (Menidia menidia) has been the focus of extensive research efforts in ecology, evolutionary biology, and physiology over the past three decades, but lack of genomic resources has so far hindered examination of the molecular basis underlying the remarkable patterns of phenotypic variation described in this species. We here present the first reference transcriptome for M. menidia
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The genome of Ectocarpus subulatus – A highly stress-tolerant brown alga Mar. Genom. (IF 1.672) Pub Date : 2020-01-11 Simon M. Dittami, Erwan Corre, Loraine Brillet-Guéguen, Agnieszka P. Lipinska, Noé Pontoizeau, Meziane Aite, Komlan Avia, Christophe Caron, Chung Hyun Cho, Jonas Collén, Alexandre Cormier, Ludovic Delage, Sylvie Doubleau, Clémence Frioux, Angélique Gobet, Irene González-Navarrete, Agnès Groisillier, Cécile Hervé, Thierry Tonon
Brown algae are multicellular photosynthetic stramenopiles that colonize marine rocky shores worldwide. Ectocarpus sp. Ec32 has been established as a genomic model for brown algae. Here we present the genome and metabolic network of the closely related species, Ectocarpus subulatus Kützing, which is characterized by high abiotic stress tolerance. Since their separation, both strains show new traces
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The isolation and genome sequencing of a novel cyanophage S-H68 from the Bohai Sea, China. Mar. Genom. (IF 1.672) Pub Date : 2020-01-02 Chenglong Xue,Xinxin Liu,Qi Wang,Tongtong Lin,Min Wang,Qian Liu,Hongbing Shao,Yong Jiang
Cyanobacteria, also known as bule-green algae, are capable of photosynthesis and have a fixed carbon and nitrogen effect. The virus that specifically infects cyanobacteria is called the cyanophage. Cyanophages play a key role in building microbial communities. However, only a small number of cyanophages have been reported so far. In this study, a novel Synechococcus cyanophage S-H68 was isolated from
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Cytogenetic characterization of the Antarctic silverfish Pleuragramma antarctica (Boulenger 1902) through analysis of mitotic chromosomes from early larvae Mar. Genom. (IF 1.672) Pub Date : 2019-12-28 Laura Ghigliotti, Chi-Hing C. Cheng, Catherine Ozouf-Costaz, Chantal Guidi-Rontani, Marino Vacchi, Sara Federici, Eva Pisano
This paper describes the cytogenetic features of the Antarctic silverfish Pleuragramma antarctica (Boulenger 1902), a keystone species of the Antarctic coastal marine ecosystem. Conventional cytogenetic analyses and physical mapping of repetitive DNA sequences were performed on metaphase plates obtained through direct chromosome preparation from P. antarctica early larvae. The Antarctic silverfish
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Short communication: Characterization of the expression of microRNAs in the poecilogonous polychaete B. wellingtonensis Mar. Genom. (IF 1.672) Pub Date : 2019-12-26 Alvaro Figueroa, Leyla Cárdenas, Martin Caicedo, Fernanda X. Oyarzun, Daniel Doherty-Weason, Antonio Brante
Poecilogony is a type of reproduction in which a species produces different types of larvae. Boccardia wellingtonensis, is a poecilogonous polychaete with females producing planktotrophic and adelphophagic larvae, in addition to nurse eggs, in the same capsule that differ in feeding behavior. It is still unclear why planktotrophs do not feed on nurse eggs during the intracapsular development and arrest
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Microscopic ossicle analyses and the complete mitochondrial genome sequence of Holothuria (Roweothuria) polii (Echinodermata; Holothuroidea) provide new information to support the phylogenetic positioning of this sea cucumber species Mar. Genom. (IF 1.672) Pub Date : 2019-12-19 Valerio Joe Utzeri, Anisa Ribani, Samuele Bovo, Valeria Taurisano, Matteo Calassanzio, David Baldo, Luca Fontanesi
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De novo transcriptome assembly of the Qatari pearl oyster Pinctada imbricata radiata Mar. Genom. (IF 1.672) Pub Date : 2019-12-07 Tim P. Bean, Zenaba Khatir, Brett P. Lyons, Ronny van Aerle, Diana Minardi, John P. Bignell, David Smyth, Bruno Welter Giraldes, Alexandra Leitão
The pearl oyster Pinctada imbricata radiata is an iconic species in Qatar, representing an integral part of the nation's cultural heritage and one of the main economic foundations upon which the nation developed. During the early part of the 20th century, nearly half the Qatar population was involved in the pearl oyster industry. However, the fishery has undergone steady decline since the 1930s, and
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Genome analysis of Crassaminicella sp. SY095, an anaerobic mesophilic marine bacterium isolated from a deep-sea hydrothermal vent on the Southwest Indian Ridge. Mar. Genom. (IF 1.672) Pub Date : 2019-11-27 Xue-Gong Li,Wei-Jia Zhang,Xiao-Qing Qi,Long-Fei Wu
Crassaminicella sp. strain SY095 is an anaerobic mesophilic marine bacterium that was recently isolated from a deep-sea hydrothermal vent on the Southwest Indian Ridge. Here, we present the complete genome sequence of strain SY095. The genome consists of a chromosome of 3,046,753 bp (G + C content of 30.81%) and a plasmid of 36,627 bp (G + C content of 31.29%), encodes 2966 protein, 135 tRNA genes
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t-Distributed Stochastic Neighbor Embedding (t-SNE): A tool for eco-physiological transcriptomic analysis Mar. Genom. (IF 1.672) Pub Date : 2019-11-26 Matthew C. Cieslak, Ann M. Castelfranco, Vittoria Roncalli, Petra H. Lenz, Daniel K. Hartline
High-throughput RNA sequencing (RNA-Seq) has transformed the ecophysiological assessment of individual plankton species and communities. However, the technology generates complex data consisting of millions of short-read sequences that can be difficult to analyze and interpret. New bioinformatics workflows are needed to guide experimentation, environmental sampling, and to develop and test hypotheses
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De novo transcriptome sequencing of the thecate colonial hydrozoan, Dynamena pumila Mar. Genom. (IF 1.672) Pub Date : 2019-11-24 Daria Kupaeva, Evgenii Konorov, Stanislav Kremnyov
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Looking for the hidden: Characterization of lysogenic phages in potential pathogenic Vibrio species from the North Sea Mar. Genom. (IF 1.672) Pub Date : 2019-11-19 Alexa Garin-Fernandez, Antje Wichels
The incidence of potentially pathogenic Vibrio species in the marine environment around Europe, is correlated with the increase of surface seawater temperature. Despite their importance, little is known about the trigger factors of potential outbreak-causing strains in this region. As prophages may compose a major reservoir of virulence traits in marine ecosystems, this study aims to identify and characterize
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Adaptations to environmental change: Globin superfamily evolution in Antarctic fishes Mar. Genom. (IF 1.672) Pub Date : 2019-11-14 Jacob M. Daane, Daniela Giordano, Daniela Coppola, Guido di Prisco, H. William Detrich, Cinzia Verde
The ancient origins and functional versatility of globins make them ideal subjects for studying physiological adaptation to environmental change. Our goals in this review are to describe the evolution of the vertebrate globin gene superfamily and to explore the structure/function relationships of hemoglobin, myoglobin, neuroglobin and cytoglobin in teleost fishes. We focus on the globins of Antarctic
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Globins and nitric oxide homeostasis in fish embryonic development Mar. Genom. (IF 1.672) Pub Date : 2019-11-08 Elizabeth R. Rochon, Paola Corti
Since the discovery of new members of the globin superfamily such as Cytoglobin, Neuroglobin and Globin X, in addition to the most well-known members, Hemoglobin and Myoglobin, different hypotheses have been suggested about their function in vertebrates. Globins are ubiquitously found in living organisms and can carry out different functions based on their ability to bind ligands such as O2, and nitric
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Complete genome sequence of Dyadobacter sp. 32, isolated from a culture of the freshwater diatom Cymbella microcephala Mar. Genom. (IF 1.672) Pub Date : 2019-11-05 Lachlan Dow, Kathryn Lee Morrissey, Anne Willems, Peter G. Kroth
Bacteria have been shown to be involved in different species-specific interactions with eukaryotic algae such as diatoms, impacting important ecosystem processes. Recently, a strain assigned to Dyadobacter, named ‘species 32’, has been shown to be involved in a number of ecologically relevant diatom processes, such as biofilm formation or growth enhancement, depending on the diatom species. This bacterium
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Environmental regulation of the function of circulating erythrocytes via changes in age distribution in teleost fish: Possible mechanisms and significance Mar. Genom. (IF 1.672) Pub Date : 2019-10-31 Mikko Nikinmaa
The blood of fish has a continuous age distribution of erythrocytes. The properties of young and old erythrocytes differ with young erythrocytes being functionally much more versatile than old erythrocytes, which have higher haemoglobin content. Factors which affect the formation and breakdown of erythrocytes are reviewed. Erythropoiesis in fish is largely similar to that in mammals.